In animals, myostatin (MSTN) is a negative regulator that inhibits muscle growth and repair. The decreased level of functional MSTN gene expression can change the amount and proportions of fats in pigs. In this study we determined the lipidomics of subcutaneous fat in MSTN single copy mutant pigs and evaluated the variations in lipid contents of the subcutaneous fat from MSTN+/− and wild type Large White (LW) pigs via ultra-performance liquid chromatography–quadrupole/Orbitrap-mass spectrometry (MS). The results showed that the quantities of glycerolipids, sphingolipids, fatty acyls and glycerophospholipids were significantly changed, particularly, the molecular diacylglycerol in glycerolipids, long-chain unsaturated fatty acids, and ceramide non-hydroxy fatty acid-sphingosine in sphingolipids were remarkably increased in the MSTN+/− group. Due to their positive bioavailability demonstrated by previous researches, these three lipids might be beneficial for human health. Further, the results of our study confirm that MSTN participates in the regulation of fat metabolism, and reduced expression of MSTN can ultimately influence the accumulation of lipid contents in the subcutaneous fat of pigs.